The reason for having a battery isolator is so that your system will **** power only from the secondary battery when the car is off, so both of your batts wont be ran down and your car fail to start. When the car is started, its started off the primary battery, once the car is running , both of the batteries are in the loop, neither is isolated, so your system draws power from both and the alternator charges both. So when the car is turned off, the secondary battery goes back to being isolated, only the secondary battery will be powering your system, and the primary batt is left alone so it can save its power for starts. When the isolator is used and the car is off, the primary batt is used only for starting, the secondary batt is only used for stereo power. Once the car is on and running, both batts are being used and charged. I know i repeated myself alot there, just wanted to be clear. You can get by perfectly fine without an isolator, just as long as you dont run down your primary batt low enough for your car not to start. An isolator is just used to insure your primary batt isnt drained when the car is off.
Hope that helps.